> Is it possible that during the boot sequence scp doesn't look in the right 
> place for the trusted host file ?

 A boot environment and a login environment are very different things.
 For instance, in your boot environment, you have no defined USER or
HOME environment variables. scp has no way of knowing that your
known_hosts file is in /root/.ssh if there's no HOME=/root variable
to tell it so.
 Adjust the environment in your scp command line. Make sure it does
not leak to the rest of the boot scripts, though.

-- 
 Laurent

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